.Rbuildignore

@@ -7,3 +7,4 @@
 ^inst/application/_utilities/MDR/XLSX$
 ^inst/application/_utilities/MDR/XSD$
 ^inst/application/_utilities/MDR/\.~lock\.mdr\.csv#$
+^\.gitlab-ci\.yml$

.gitignore

@@ -19,6 +19,7 @@
 !/inst/
 !/man/
 !/NAMESPACE
+!/.gitlab-ci.yml
 /inst/application/_settings/
 .Rproj.user
 *.Rproj

.gitlab-ci.yml

+variables:
+  _R_CHECK_CRAN_INCOMING_: "false"
+  _R_CHECK_FORCE_SUGGESTS_: "true"
+  CI_IMAGE_NAME: "rocker/verse"
+  CI_IMAGE_TAG: "3.6.1"
+  R_PKG_NAME: "miRacumDQA"
+
+default:
+  image: ${CI_IMAGE_NAME}:${CI_IMAGE_TAG}
+  before_script:
+    - echo "options('repos' = 'https://ftp.fau.de/cran/')" >> /usr/local/lib/R/etc/Rprofile.site
+    - R -e "devtools::install_dev_deps(pkg = '.', upgrade = 'always')"
+    - mkdir -p ci
+
+stages:
+  - build
+  - test
+  - deploy
+
+check:
+  stage: build
+  allow_failure: true # necessary when having development-packages (in remotes-section of DESCRIPTION)
+  script:
+    - R -e "devtools::check(pkg = '.', args = c('--no-tests'), build_args = c('--no-build-vignettes'), check_dir = '${CI_PROJECT_DIR}/ci')"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.Rcheck"
+    when: on_failure # upload check artifacts when job fails!
+    expire_in: 1 week
+
+create_manual:
+  stage: build
+  script:
+    - R -e "devtools::build_manual(pkg = '.', path = '${CI_PROJECT_DIR}/ci')"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.pdf"
+    expire_in: 1 week
+
+build_source:
+  stage: build
+  script:
+    - R -e "devtools::build(pkg = '.', path = '${CI_PROJECT_DIR}/ci', binary = FALSE, vignettes = FALSE)"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.tar.gz"
+    expire_in: 1 week
+
+build_binary:
+  stage: build
+  script:
+    - R -e "devtools::build(pkg = '.', path = '${CI_PROJECT_DIR}/ci', binary = TRUE, vignettes = FALSE)"
+  artifacts:
+    paths:
+      - "${CI_PROJECT_DIR}/ci/*.tar.gz"
+    expire_in: 1 week
+
+# To have the coverage percentage appear as a gitlab badge follow these
+# instructions:
+# https://docs.gitlab.com/ee/user/project/pipelines/settings.html#test-coverage-parsing
+# The coverage parsing string is
+# Coverage: \d+\.\d+
+
+coverage:
+  stage: test
+  allow_failure: true
+  when: on_success
+  script:
+    - R -e "install.packages('DT')"
+    - R -e "covr::gitlab(quiet = FALSE)"
+  artifacts:
+    paths:
+      - public
+
+testing:
+  stage: test
+  allow_failure: true
+  when: on_success
+  script:
+    - R -e "devtools::test(pkg = '.')"
+
+# To produce a code coverage report as a GitLab page see
+# https://about.gitlab.com/2016/11/03/publish-code-coverage-report-with-gitlab-pages/
+
+install:
+  stage: deploy
+  script:
+    - R -e "devtools::install(pkg = '.', upgrade = 'always')"

DESCRIPTION

 Package: miRacumDQA
 Title: MIRACUM DQA Tool
-Version: 2.0.0
+Version: 2.0.1
 Authors@R: 
     c(person(given = "Lorenz A.",
              family = "Kapsner",
@@ -16,11 +16,12 @@ URL: https://gitlab.miracum.org/miracum-dqa/miRacumDQA
 BugReports: https://gitlab.miracum.org/miracum-dqa/miRacumDQA/issues
 Encoding: UTF-8
 Copyright: Universitätsklinikum Erlangen
-Date/Publication: 2019-09-26 06:21:25 UTC
+Date: 2019-11-12
 Imports: 
-    shiny,
-    DQAstats (>= 0.0.2),
-    DQAgui (>= 0.0.2)
+    shiny
+Remotes: 
+    url::https://gitlab.miracum.org/miracum-dqa/dqagui/-/archive/v0.0.3/dqagui-v0.0.3.zip,
+    url::https://gitlab.miracum.org/miracum-dqa/dqastats/-/archive/v0.0.3/dqastats-v0.0.3.zip
 Suggests: 
     testthat,
     processx

NAMESPACE

 # Generated by roxygen2: do not edit by hand
 
 export(launchDQAtool)
-import(DQAgui)
 import(shiny)

R/launch_app.R

@@ -17,26 +17,61 @@
 #' @title Launch the MIRACUM DQA Tool
 #'
 #' @param port The port, the MIRACUM DQA Tool is running on (default: 3838)
-#' @param utilspath The path to the utilities-folder, containing the metadata repository files (`mdr.csv` inside the folder `MDR`),
-#'   JSON files with SQL statements (inside the folder `SQL`), config files for the database connection (`settings_default.yml`)
-#'   and the email address used for the data map (`email.yml`), a JSON file containing site names (inside the folder `MISC`) and a
-#'   markdown templated to create the PDF report (`DQA_report.Rmd` inside the folder `RMD`).
-#' @param db_source The name of the source database. Currently, the only allowed argument is `p21csv` used for the import of the
+#' @param utilspath The path to the utilities-folder, containing the metadata
+#'   repository files (`mdr.csv` inside the folder `MDR`), JSON files with
+#'   SQL statements (inside the folder `SQL`), config files for the database
+#'   connection (`settings_default.yml`) and the email address used for the
+#'   data map (`email.yml`), a JSON file containing site names (inside the
+#'   folder `MISC`) and a markdown templated to create the PDF report
+#'   (`DQA_report.Rmd` inside the folder `RMD`).
+#' @param db_source The name of the source database. Currently, the only
+#'   allowed argument is `p21csv` used for the import of the
 #'   corresponding csv files.
 #'
 #' @return the MIRACUM DQA Tool Shiny application
 #'
-#' @import DQAgui shiny
+#' @import shiny
 #'
 #' @export
 #'
 
-launchDQAtool <- function(port=3838, utilspath, db_source){
+launchDQAtool <- function(port=3838,
+                          utilspath,
+                          db_source){
+
+
+  global_env_hack <- function(key,
+                              val,
+                              pos) {
+    assign(
+      key,
+      val,
+      envir = as.environment(pos)
+    )
+  }
+
+  global_env_hack(
+    key = "utilspath",
+    val = utilspath,
+    pos = 1L
+  )
+
+  global_env_hack(
+    key = "db_source",
+    val = db_source,
+    pos = 1L
+  )
+
   options(shiny.port = port)
-  assign("utilspath", utilspath, envir = .GlobalEnv)
-  assign("db_source", db_source, envir = .GlobalEnv)
 
-  shiny::shinyAppDir(appDir = system.file("application", package = "miRacumDQA"))
+
+  cat(paste0("\nVersion DQAstats: ", utils::packageVersion("DQAstats"),
+             "\nVersion DQAgui: ", utils::packageVersion("DQAgui"),
+             "\n"))
+
+  shiny::shinyAppDir(
+    appDir = system.file("application", package = "miRacumDQA")
+  )
 }
 
 # debugging

data-raw/devstuffs.R

@@ -16,13 +16,13 @@ my_desc$set("Copyright", "Universitätsklinikum Erlangen")
 # Remove some author fields
 my_desc$del("Maintainer")
 # Set the version
-my_desc$set_version("2.0.0")
+my_desc$set_version("2.0.1")
 # The title of your package
 my_desc$set(Title = "MIRACUM DQA Tool")
 # The description of your package
 my_desc$set(Description = "The MIRACUM consortium's data quality assessment tool.")
 # The description of your package
-my_desc$set("Date/Publication" = paste(as.character(Sys.time()), "UTC"))
+my_desc$set("Date" = as.character(Sys.Date()))
 # The urls
 my_desc$set("URL", "https://gitlab.miracum.org/miracum-dqa/miRacumDQA")
 my_desc$set("BugReports",
@@ -52,8 +52,15 @@ usethis::use_gpl3_license(name="Universitätsklinikum Erlangen")
 
 # Imports
 usethis::use_package("shiny", type = "Imports")
-usethis::use_dev_package("DQAstats", type = "Imports")
-usethis::use_dev_package("DQAgui", type = "Imports")
+
+# Development package
+# https://cran.r-project.org/web/packages/devtools/vignettes/dependencies.html
+devtools::install_git(url = "https://gitlab.miracum.org/miracum-dqa/dqastats.git", ref = "v0.0.3", upgrade = "always")
+devtools::install_git(url = "https://gitlab.miracum.org/miracum-dqa/dqagui.git", ref = "v0.0.3", upgrade = "always")
+desc::desc_set_remotes(c("url::https://gitlab.miracum.org/miracum-dqa/dqagui/-/archive/v0.0.3/dqagui-v0.0.3.zip",
+                         "url::https://gitlab.miracum.org/miracum-dqa/dqastats/-/archive/v0.0.3/dqastats-v0.0.3.zip"),
+                       file = usethis::proj_get())
+
 
 # Suggests
 usethis::use_package("testthat", type = "Suggests")

docker/Dockerfile

-# https://hub.docker.com/r/rocker/shiny/
-FROM rocker/shiny-verse
+FROM rocker/shiny-verse:3.6.1
 
 # install necessary system dependencies for r packages (e.g. devtools, RPostgres)
 RUN apt-get update && apt-get install -y --no-install-recommends \
@@ -13,22 +12,22 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     gpg-agent \
     git
 
-
-ARG p_base="devtools \
-    tinytex"
-
-RUN for package in $p_base; do \
-    R -q -e "p <- \"$package\"; if (isFALSE(p %in% installed.packages()[,\"Package\"])){; cat(paste(\"Installing package:\", p, \"\n\n\")); install.packages(p, repos = \"https://ftp.fau.de/cran/\", quiet=T);} else {;cat(paste(\"Package\", p, \"is already installed\n\n\"));}"; \
-    done
+# set cran repo
+RUN echo "options('repos' = 'https://ftp.fau.de/cran/')" >> /usr/local/lib/R/etc/Rprofile.site
 
 # install tinytex
+RUN R -q -e "remotes::update_packages(packages = \"tinytex\", upgrade = \"always\")"
+
 USER shiny
-RUN R -q -e 'tinytex::install_tinytex()'
+RUN R -q -e "tinytex::install_tinytex()"
 USER root
 
+ENV PATH="/home/shiny/bin:${PATH}"
+
 # install required LaTeX-Packages
-RUN ./home/shiny/.TinyTeX/bin/x86_64-linux/tlmgr update --self
-RUN ./home/shiny/.TinyTeX/bin/x86_64-linux/tlmgr install \
+RUN tlmgr option repository http://mirror.ctan.org/systems/texlive/tlnet && \
+    tlmgr update --self && \
+    tlmgr install \
     multirow \
     xcolor \
     colortbl \
@@ -59,11 +58,7 @@ RUN ./home/shiny/.TinyTeX/bin/x86_64-linux/tlmgr install \
     latex-graphics-dev \
     geometry \
     ec \
-    ifxetex \
-    ifluatex
-
-# add TeX-installation to PATH
-ENV PATH="/home/shiny/bin:${PATH}"
+    iftex
 
 # repository name
 ARG REPO_NAME=dqastats

docker/build_image.sh

@@ -5,9 +5,9 @@ mkdir addfolder
 cd addfolder
 
 # clone repositories
-git clone -b v0.0.2 https://gitlab.miracum.org/miracum-dqa/dqastats.git
-git clone -b v0.0.2 https://gitlab.miracum.org/miracum-dqa/dqagui.git
-git clone -b v2.0.0 https://gitlab.miracum.org/miracum-dqa/miracumdqa.git
+git clone -b v0.0.3 https://gitlab.miracum.org/miracum-dqa/dqastats.git
+git clone -b v0.0.3 https://gitlab.miracum.org/miracum-dqa/dqagui.git
+git clone -b v2.0.1 https://gitlab.miracum.org/miracum-dqa/miracumdqa.git
 cd ..
 
 docker build -f Dockerfile -t dqa-miracum .

docker/deploy_image.sh

@@ -17,9 +17,9 @@ printf "\n\ncloning repo ...\n"
 mkdir addfolder
 cd addfolder
 # clone repository
-git clone -b v0.0.2 https://gitlab.miracum.org/miracum-dqa/dqastats.git
-git clone -b v0.0.2 https://gitlab.miracum.org/miracum-dqa/dqagui.git
-git clone -b v2.0.0 https://gitlab.miracum.org/miracum-dqa/miracumdqa.git
+git clone -b v0.0.3 https://gitlab.miracum.org/miracum-dqa/dqastats.git
+git clone -b v0.0.3 https://gitlab.miracum.org/miracum-dqa/dqagui.git
+git clone -b v2.0.1 https://gitlab.miracum.org/miracum-dqa/miracumdqa.git
 cd ..
 
 printf "\n\nbuilding images ...\n"

docker/docker-compose.dqatool.yml

@@ -3,14 +3,14 @@ version: '3'
 services:
   dqatool:
     container_name: dqa-miracum
-    image: docker.miracum.org/dqa/miracumdqa:2.0.0
+    image: docker.miracum.org/dqa/miracumdqa:2.0.1
     restart: unless-stopped
     volumes:
       - /home/i2b2/start/Input:/home/input
     ports:
-    - "3838:3838"
+      - "3838:3838"
     networks:
-    - miracum-net
+      - miracum-net
 
 networks:
     miracum-net:

docker/push_harbor.sh

 #!/bin/bash
 
-./deploy_image.sh docker.miracum.org/dqa miracumdqa 2.0.0
+./deploy_image.sh docker.miracum.org/dqa miracumdqa 2.0.1

inst/application/_utilities/RMD/_header/header.tex

@@ -18,7 +18,7 @@
 \usepackage{caption}
 \captionsetup[figure]{labelformat=empty}
 \usepackage[ngerman]{babel}
-\usepackage{graphicx,grffile}
+\usepackage{graphicx}
 \usepackage{float}
 \usepackage{pdflscape}
 \usepackage{longtable}

inst/application/_utilities/RMD/_header/miracum.latex

@@ -124,7 +124,11 @@ $if(tables)$
 \usepackage{longtable,booktabs}
 $endif$
 $if(graphics)$
-\usepackage{graphicx,grffile}
+\usepackage{graphicx}
+% grffile has become a legacy package: https://ctan.org/pkg/grffile
+\IfFileExists{grffile.sty}{%
+\usepackage{grffile}
+}{}
 \makeatletter
 \def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
 \def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
@@ -199,7 +203,7 @@ $if(compact-title)$
 \usepackage{titling}
 
 % Create subtitle command for use in maketitle
-\newcommand{\subtitle}[1]{
+\providecommand{\subtitle}[1]{
   \posttitle{
     \begin{center}\large#1\end{center}
     }
@@ -279,7 +283,6 @@ $endif$
 \setcounter{tocdepth}{$toc-depth$}
 \tableofcontents
 }
-\newpage
 $endif$
 $if(lot)$
 \listoftables

man/launchDQAtool.Rd

@@ -9,12 +9,16 @@ launchDQAtool(port = 3838, utilspath, db_source)
 \arguments{
 \item{port}{The port, the MIRACUM DQA Tool is running on (default: 3838)}
 
-\item{utilspath}{The path to the utilities-folder, containing the metadata repository files (`mdr.csv` inside the folder `MDR`),
-JSON files with SQL statements (inside the folder `SQL`), config files for the database connection (`settings_default.yml`)
-and the email address used for the data map (`email.yml`), a JSON file containing site names (inside the folder `MISC`) and a
-markdown templated to create the PDF report (`DQA_report.Rmd` inside the folder `RMD`).}
+\item{utilspath}{The path to the utilities-folder, containing the metadata
+repository files (`mdr.csv` inside the folder `MDR`), JSON files with
+SQL statements (inside the folder `SQL`), config files for the database
+connection (`settings_default.yml`) and the email address used for the
+data map (`email.yml`), a JSON file containing site names (inside the
+folder `MISC`) and a markdown templated to create the PDF report
+(`DQA_report.Rmd` inside the folder `RMD`).}
 
-\item{db_source}{The name of the source database. Currently, the only allowed argument is `p21csv` used for the import of the
+\item{db_source}{The name of the source database. Currently, the only
+allowed argument is `p21csv` used for the import of the
 corresponding csv files.}
 }
 \value{